Error loading file saved from ImSpector

[Powerfultool]

Hi - I got this error trying to load a file produced by saving an OME-TIFF of widefield time-gated FLIM data from ImSpector (the LaVision TriMScope control software), using 5.0.1RC-20 on Windows 7

============================== Index exceeds matrix dimensions.

Error in flim_data_series/get_image_dimensions (line 203)

Error in flim_data_series/load_multiple (line 30)

Error in flim_data_series/load_single (line 104)

Error in flim_data_series_controller/load_single (line 159)

Error in front_end_menu_controller/menu_file_load_single_callback (line 650)

Error in front_end_menu_controller>@(varargin)obj.menu_file_load_single_callback(varargin{:})

Error in escaped_callback (line 7)

Error in front_end_menu_controller>@(x,y)escaped_callback(fcn) (line 261)

[seanwarren]

Hi @Powerfultool, please could you try with the 5.0.3 release version of FLIMfit? If you still have problems please could you send me the offending file

Cheers Sean

[Powerfultool]

Hi Sean,

Just gave it a go, and got what looks like an identical error. Will send you the file shortly.

Regards, Sunil

[seanwarren]

Cheers, I'll have a look. The OME tiffs LaVision write a bit a of an unholy mess, they seem to be a bit different for each experiment. Any idea what you are expecting in the file?

[Powerfultool]

It's a worse-than average pain, I'm guessing... This file's from a quenched fluorescein IRF sample, but in true ImSpector style you can only use 256 delays for any one acquisition, so in reality it's only the first half of the IRF... Basically, there should be a bright rectangle a bit to the right of the image centre, and it should look fairly time-gated IRF-like on the t-axis.

[seanwarren]

Hi Sunil, perhaps unsurprisingly it looks the format for the LaVision time gated data is different from a real OME.TIFF in an new and interesting way. I should be able to extract it correctly but probably not going to happen this evening I'm afraid!

[Powerfultool]

No worries - have a good evening! Let me know if there's anything useful we can do at this end (I'll be away on conference from Friday for a week, but Elizabeth might be able to get anything you need)

[seanwarren]

No I think that's all I need - I can see the delay values in the XML here so should be fine

[Powerfultool]

Yeah, so there's also a little wriggle with that - because ImSpector doesn't let you apply a calibration file, those values are what we told it to try and linearise the gate spacing... they should correspond to 25 ps intervals going up from zero. I don't suppose there's any way to easily overwrite those?

[imunro]

Hi Both I did some preliminary work on this - see https://github.com/imunro/FLIMfit/commit/b2c9a7d2a322eb4fd3466455e70fcf07efe8b98b whether it'll be useful depends, I suspect, on how much @Powerfultool 's acquisition protocol has changed since then.

[seanwarren]

Yes you can apply a time point calibration file the same way we used for the HRIs back in the day, it's basically just a csv file with a nominal->real time mapping in two columns. I'll run you through it when we get your files loaded.

Cheers Sean

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On Wed, Jun 21, 2017 at 8:52 PM +1000, "Powerfultool" notifications@github.com<mailto:notifications@github.com> wrote:

Yeah, so there's also a little wriggle with that - because ImSpector doesn't let you apply a calibration file, those values are what we told it to try and linearise the gate spacing... they should correspond to 25 ps intervals going up from zero. I don't suppose there's any way to easily overwrite those?

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[imunro]

@seanwarren let me know if you need me to raise a PR from my changes above.

[seanwarren]

Yes please Ian - looks like that should get us most of the way there

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On Wed, Jun 21, 2017 at 10:50 PM +1000, "imunro" notifications@github.com<mailto:notifications@github.com> wrote:

@seanwarrenhttps://github.com/seanwarren let me know if you need me to raise a PR from my changes above.

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[imunro]

https://github.com/flimfit/FLIMfit/pull/325

[seanwarren]

Hi Sunil, please could you try this version: https://storage.googleapis.com/flimfit-downloads/merge/5.0.3-3-g970816a1/FLIMfit%205.0.3-3-g970816a1%20Setup%20x64.exe

It's reading the files correctly here.

Cheers Sean

[seanwarren]

Apologies, the correct version is here: https://storage.googleapis.com/flimfit-downloads/merge/5.0.3-4-gc1a3585a/FLIMfit%205.0.3-4-gc1a3585a%20Setup%20x64.exe

[Powerfultool]

Hi Sean – sorry for taking a while to reply – have been at a conference… I’ve just had a chance to give this version a try, and there’s a couple of things that seem a bit off – if you load a folder with multiple images (a lifetime z-stack in this case), it offers you the choice of which images to open, but it looks like it just opens multiple copies of the first file… Also, it looks like the fit seems normal on the decay screen, but gives a negative lifetime and I0 (see attached)…

Regards, Sunil

[cid:image001.png@01D2F4D5.3D9E94A0] [cid:image002.png@01D2F4D5.3D9E94A0] [cid:image003.png@01D2F4D5.3D9E94A0]

From: Sean Warren [mailto:notifications@github.com] Sent: 23 June 2017 03:44 To: flimfit/FLIMfit Cc: Kumar, Sunil; Mention Subject: Re: [flimfit/FLIMfit] Error loading file saved from ImSpector (#324)

Apologies, the correct version is here: https://storage.googleapis.com/flimfit-downloads/merge/5.0.3-4-gc1a3585a/FLIMfit%205.0.3-4-gc1a3585a%20Setup%20x64.exe

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/flimfit/FLIMfit/issues/324#issuecomment-310556028, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI2vujIwrrYKd6fww3YdBblEeHJ28YWBks5sGyZcgaJpZM4OAuXB.

[imunro]

You have to be careful here. The LaVision code seems (from Anca;s stuff) to generate filesets. ie you may get n ome.tifs but Bio-formats sees them as single 'set' so clicking on any of them will open them all, if that makes sense.

[Powerfultool]

I think that’s what it’s doing (opening filesets – it does come up with a list with checkboxes), but although all the images have different filenames, they all look the same, whereas if you open them in ImageJ, you can see that they’re different…

From: imunro [mailto:notifications@github.com] Sent: 04 July 2017 16:00 To: flimfit/FLIMfit Cc: Kumar, Sunil; Mention Subject: Re: [flimfit/FLIMfit] Error loading file saved from ImSpector (#324)

You have to be careful here. The LaVision code seems (from Anca;s stuff) to generate filesets. ie you may get n ome.tifs but Bio-formats sees them as single 'set' so clicking on any of them will open them all, if that makes sense.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/flimfit/FLIMfit/issues/324#issuecomment-312898929, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI2vus-maKYY_rLKn-fB0XAzWpF39AlZks5sKlNkgaJpZM4OAuXB.

[imunro]

You may only need to select one file though. If you select all of a fileset FLIMfit might get confused - & it won't be alone.

[Powerfultool]

Ah, got it – just opening one file also gives you the options, but you have to tick through everything manually to load them all, which probably won’t be too much fun on big datasets… maybe a ‘select all’ button would help? Also, the z-planes are showing up as channels, because why not…

From: imunro [mailto:notifications@github.com] Sent: 04 July 2017 16:18 To: flimfit/FLIMfit Cc: Kumar, Sunil; Mention Subject: Re: [flimfit/FLIMfit] Error loading file saved from ImSpector (#324)

You may only need to select one file though. If you select all of a fileset FLIMfit might get confused - & it won't be alone.

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[imunro]

I think there is a "select all" button for Z & T but not channels. Having sad that looks like we have some sort of channelZ mix-up.I'll have a look tomorrow.

[Powerfultool]

Cool – thanks!

From: imunro [mailto:notifications@github.com] Sent: 04 July 2017 17:24 To: flimfit/FLIMfit Cc: Kumar, Sunil; Mention Subject: Re: [flimfit/FLIMfit] Error loading file saved from ImSpector (#324)

I think there is a "select all" button for Z & T but not channels. Having sad that looks like we have some sort of channelZ mix-up.I'll have a look tomorrow.

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[imunro]

Having just looked at some of the data in question FLIMfit seems to be doing it's job (guessing which dimension is the t FLIM one) correctly and the channels are actually written as Channels in this file. Ideally we could find a way to configure the LaVision software to use at least one dimension correctly. Failing that all I can suggest add a "select all" button to Channels as for Z and T.

[imunro]

@Powerfultool could you try this one when you have a chance https://storage.googleapis.com/flimfit-downloads/merge/5.0.3-9-g576562b6/FLIMfit%205.0.3-9-g576562b6%20Setup%20x64.exe